I have a couple of levels when dealing with Calibre:
Tags, which are basically just
Fiction.Mystery.Cozy Mystery,
Fanfiction.Crossovers, or
Nonfiction.Hobbies & Recreation.Food & Drink.Cookbooks. I use these for navigating in the tag browser.
Genres is a composite column which is basically just the tags split apart and deduped - e.g. for one cozy mystery series, it comes out as
American South, Animals, Cats, Cozy Mystery, Fiction, Mystery, United States. This has an unintended benefit that if I click on, say, "Cats," I get both fiction
and nonfiction books related to it.

I display these in the book details instead of Tags.
Fandom is for fanfiction, and populated by FanFicFare. I used KoboTouchExtended to have my Kobo display a subtitle with the fandom and fanfic status (whether it's complete or still in-progress).
Documenation Type is an enumerated (dropdown) column for documentation & manuals, and it has preset categories:
Software Manuals, Game Manuals, Other Manuals, Supplementals, Official Strategy Guides, Unofficial Strategy Guides, and
Artbooks & Lore.
Kobo Path. Another composite column. It's just the top level of the tags -
Comics, Documentation & Manuals, Fanfiction, Fiction, Magazines & Periodicals, and
Nonfiction. This is used for the save template for sending to my Kobo (it was preferable to having 100+ author folders in the root of the drive).
Kobo Collection. This is just shelves on my Kobo synced with the KoboTouchExtended driver, and manually done (though I am trying to automate the process by using Action Chains to determine the shelves from existing values in Genre). I also use it to mark the non-sideloaded books (I have a shelf called "Kobo Store") and show an icon so I remember not to overwrite them.